* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html This animation from Malcolm Campbell may also be helpful.]

* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html This animation from Malcolm Campbell may also be helpful.]

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==== Answer the following Discovery Questions from Chapter 4====

==== Answer the following Discovery Questions from Chapter 4====

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'''5.''' (p. 110) Choose two genes from Figure 4.6 [https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_21252_1%26url%3D (PDF of figures on MyLMUConnect)] and draw a graph to represent the change in transcription over time.

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'''5.''' (p. 110) Choose two genes from Figure 4.6 [https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_57614_1%26url%3D (PDF of figures on MyLMUConnect)] and draw a graph to represent the change in transcription over time.

'''<nowiki>*</nowiki>Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.'''

'''<nowiki>*</nowiki>Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.'''

Current revision

This journal entry is due on Thursday, March 15 at midnight PDT(Wednesday night/Thursday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Answer the following Discovery Questions from Chapter 4

5. (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
*Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.

6b. (p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.

7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?

9. (p. 118) Why would most spots be yellow at the first time point?

10. (p. 118) Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).